Variants of chymosin with improved milk-clotting properties

ABSTRACT

Variants of chymosin with improved milk-clotting properties.

CROSS REFERENCE TO RELATED APPLICATIONS

The present application is the divisional of U.S. patent application Ser. No. 14/402,567, filed Nov. 20, 2014, which is the U.S. National Stage of International Application No. PCT/EP2013/060460, filed on May 22, 2013, which claims priority to European Patent Application No. 12169503.5, filed on May 25, 2012.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Aug. 16, 2017, is named 030427-0198_SL.txt and is 20,130 bytes in size.

FIELD OF THE INVENTION

The present invention relates to variants of chymosin with improved milk-clotting properties.

BACKGROUND ART

Enzymatic coagulation of milk by milk-clotting enzymes, such as chymosin and pepsin, is one of the most important processes in the manufacture of cheeses. Enzymatic milk coagulation is a two-phase process: a first phase where a proteolytic enzyme, chymosin or pepsin, attacks κ-casein, resulting in a metastable state of the casein micelle structure and a second phase, where the milk subsequently coagulates and forms a coagulum.

Chymosin (EC 3.4.23.4) and pepsin (EC 3.4.23.1), the milk clotting enzymes of the mammalian stomach, are aspartic proteases belonging to a broad class of peptidases.

When produced in the gastric mucosal cells, chymosin and pepsin occur as enzymatically inactive pre-prochymosin and pre-pepsinogen, respectively. When chymosin is excreted, an N-terminal peptide fragment, the pre-fragment (signal peptide) is cleaved off to give prochymosin including a pro-fragment. Prochymosin is a substantially inactive form of the enzyme which, however, becomes activated under acidic conditions to the active chymosin by autocatalytic removal of the pro-fragment. This activation occurs in vivo in the gastric lumen under appropriate pH conditions or in vitro under acidic conditions.

The structural and functional characteristics of bovine, ie Bos taurus, pre-prochymosin, prochymosin and chymosin have been studied extensively. The pre-part of the bovine pre-prochymosin molecule comprises 16 aa residues and the pro-part of the corresponding prochymosin has a length of 42 aa residues. The active bovine chymosin comprises 323 aa is a mixture of two forms, A and B, both of which are active.

Chymosin is produced naturally in mammalian species such as bovines, camels, caprines, buffaloes, sheep, pigs, humans, monkeys and rats.

Bovine chymosin has for a number of years been commercially available to the dairy industry.

WO02/36752A2 (Chr. Hansen) describes recombinant production of camel chymosin.

The references listed immediately below may in the present context be seen as references describing mutants of chymosin;

Suzuki et al: Site directed mutagenesis reveals functional contribution of Thr218, Lys220 and Asp304 in chymosin, Protein Engineering, vol. 4, January 1990, pages 69-71;

Suzuki et al: Alteration of catalytic properties of chymosin by site-directed mutagenesis, Protein Engineering, vol. 2, May 1989, pages 563-569;

van den Brink et al; Increased production of chymosin by glycosylation, Journal of biotechnology, vol. 125, September 2006, pages 304-310;

Pitts et al: Expression and characterisation of chymosin pH optima mutants produced in Tricoderma reesei, Journal of biotechnology, vol. 28, March 1993, pages 69-83;

M. G. Williams et al: Mutagenesis, biochemical characterization and X-ray structural analysis of point mutants of bovine chymosin, Protein engineering design and selection, vol. 10, September 1997, pages 991-997;

Strop et al: Engineering enzyme subsite specificity: preparation, kinetic characterization, and x-ray analysis at 2.0 ANG resolution of Val111phe site mutated calf chymosin, Biochemistry, vol. 29, October 1990, pages 9863-9871;

Supannee et &: Site-specific mutations of calf chymosin B which influence milk-dotting activity, Food Chemistry, vol. 62, June 1998, pages 133-139;

Zhang et al: Functional implications of disulfide bond, Cys45-Cys50, in recombinant prochymosin, Biochimica et biophysica acta, vol. 1343, December 1997, pages 278-286.

None of the prior art references mentioned above describe directly and unambiguously any of the chymosin mutants/variants as described/claimed below herein.

SUMMARY OF THE INVENTION

The problem to be solved by the present invention is to provide variants of chymosin with improved milk-clotting properties.

As discussed in working examples herein—the present inventors have identified a number of improved camel (see Example 6 herein) and bovine (see Example 7 herein) chymosin variants.

Based on a comparative analysis of the camel and bovine variants—the present inventors identified a number of further amino acid positions that are herein important in the sense that by making a variant in one or more of these positions one may get an improved chymosin variant (see Example 8 herein).

As known in the art—different natural wildtype chymosin polypeptide sequences obtained from different mammalian species (such as e.g. bovines, camels, sheep, pigs, or rats) are having a relatively high sequence similarity/identity.

In FIG. 1 herein this is exemplified by an alignment of herein relevant different chymosin sequences.

In view of this relatively close sequence relation ship—it is believed that the 3D structures of different natural wildtype chymosins are also relatively similar.

In the present context—a natural obtained wildtype chymosin (such as bovine chymosin or camel chymosin) may herein be an example of a parent polypeptide—i.e. a parent polypeptide to which an alteration is made to produce a variant chymosin polypeptide of the present invention.

Without being limited to theory—it is believed that the herein discussed chymosin related amino acid positions are of general importance in any herein relevant chymosin enzyme of interest (e.g. chymosins of e.g. bovines, camels, sheep, pigs, rats etc)—in the sense that by making a variant in one or more of these positions one may get en improved chymosin variant in general (e.g. an improved bovine, camel, sheep, pig or rat chymosin variant).

As discussed herein—as a reference sequence for determining the amino acid position of a parent chymosin polypeptide of interest (e.g. camel, sheep, bovine etc) is herein used the public known bovine chymosin B preprochymosin sequence (Genbank accession number P00794—disclosed as SEQ ID NO: 1 herein).

The bovine chymosin B preprochymosin of SEQ ID NO: 1 may herein alternatively be termed Bovine (Bos bovis) chymosin B or simply bovine chymosin. The sequence is also shown in FIG. 1 herein.

Another herein relevant chymosin sequence is publically known Camellus dromedarius chymosin sequence of SEQ ID NO: 2 herein. It may herein alternatively be termed camel chymosin. The sequence is also shown in FIG. 1 herein.

In the present context it is believed that a parent chymosin polypeptide (e.g. from sheep or rat) that has at least 65% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin) may herein be seen as sufficient structural related to e.g. bovine or camel chymosin in order to be improved by making a variant in any of the amino acid positions as described herein.

Accordingly, a first aspect of the invention relates to a method for making an isolated chymosin polypeptide variant comprising the steps:

(a): making en alteration at one or more positions in a parent polypeptide having chymosin activity, wherein the alteration is comprising a substitution, a deletion or an insertion in at least one amino acid position corresponding to any of positions 117, 134, 141, 143, 156, 241, 279, 280, 261, 298, 300, 307, 309, 311, 325, 350, 352 and 353; and

(b): producing and isolating the altered polypeptide of step (a) and thereby obtaining the isolated chymosin polypeptide variant, wherein the variant has chymosin activity;

and wherein:

(i): the amino acid position of the parent polypeptide is determined by an alignment of the parent polypeptide with the polypeptide of SEQ ID NO: 1 (bovine chymosin)—i.e. the polypeptide of SEQ ID NO: 1 is used to determine the corresponding amino acid sequence in the parent polypeptide; and

(ii): the parent polypeptide has at least 65% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin), which is from amino acid position 59 to amino add position 381 of SEQ ID NO: 1.

As known in the art—the skilled person may based on his common general knowledge routinely produce and purify chymosin and chymosin variants.

Said in other words, once the skilled person is in possession of a herein relevant parent polypeptide having chymosin activity of interest (e.g. from bovines, camels, sheep, pigs, or rats) it is routine work for the skilled person to make a variant of such a parent chymosin of interest.

A second aspect of the invention relates to an isolated chymosin polypeptide variant obtained by the method of first aspect or any herein relevant embodiments thereof.

The term “obtained” in relation to the second aspect above should be understood as that the isolated chymosin polypeptide variant has been obtained by the method of first aspect or any herein relevant embodiments thereof.

Accordingly, the term “obtained” in relation to the second aspect should not)e understood as obtainable.

As discussed herein—in working examples herein were made variants using the polypeptide of SEQ ID NO: 1 (Bovine) as parent polypeptide—such variant may herein be termed bovine chymosin variants.

Accordingly, a third aspect of the invention relates to an isolated chymosin polypeptide variant comprising:

(a): an alteration at one or more positions in a parent polypeptide having chymosin activity, wherein the alteration is comprising a substitution, a deletion or an insertion in at :east one amino add position corresponding to any of positions 117, 134, 14:1, 143, 156, 241, 279, 280, 281, 298, 300, 307, 309, 311, 325, 350, 352 and 353; and

(b): wherein the variant has chymosin activity;

and wherein:

(i): the amino acid position of the parent polypeptide is determined by an alignment of the parent polypeptide with the polypeptide of SEQ ID NO: 1 (bovine chymosin)—i.e. the polypeptide SEQ ID NO: 1 is used to determine the corresponding amino acid sequence in the parent polypeptide; and

(ii): the parent polypeptide has at least 90% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin), which is from amino add position 59 to amino acid position 381 of SEQ ID NO: 1; and

(iii): the isolated variant polypeptide has less than 100% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin).

As discussed herein—in working examples herein were made variants using the polypeptide of SEQ ID NO: 2 (camel chymosin) as parent polypeptide—such variant may herein be termed camel chymosin variant.

Accordingly, a fourth aspect of the invention relates to an isolated chymosin polypeptide variant comprising:

(a): an alteration at one or more positions in a parent polypeptide having chymosin activity, wherein the alteration is comprising a substitution, a deletion or an insertion in at least one amino acid position corresponding to any of positions 117, 134, 141, 143, 156, 241, 279, 280, 281, 298, 300, 307, 309, 311, 325, 350, 352 and 353; and

(b): wherein the variant has chymosin activity;

and wherein:

(i): the amino acid position of the parent polypeptide is determined by an alignment of the parent polypeptide with the polypeptide of SEQ ID NO: 1 (bovine chymosin i.e. the polypeptide of SEQ ID NO: 1 is used to determine the corresponding amino add sequence in the parent polypeptide; and

(ii): the parent polypeptide has at least 90% sequence identity with the mature polypeptide of SEQ ID NO: 2 (Camel chymosin), which is from amino acid position 59 to ammo add position 381 of SEQ ID NO: 2; and

(iii): the isolated variant polypeptide has less than 100% sequence identity with the mature polypeptide of SEQ ID NO: 2 (camel chymosin).

An isolated chymosin polypeptide variant as described herein may be used according to the art—e.g. to make a food or feed product of interest (such as e.g. a milk based product of interest that e.g. could be a cheese product).

Accordingly, a fifth aspect of the invention relates to a method for making a food or feed product comprising adding an effective amount of the isolated chymosin polypeptide variant as described herein to the food or feed ingredient(s) and carrying our further manufacturing steps to obtain the food or feed product.

Embodiment of the present invention is described below, by way of examples only.

Definitions

All definitions of herein relevant terms are in accordance of what would be understood by the skilled person in relation to the herein relevant technical context.

The term “chymosin” relates to an enzyme of the EC 3.4.23.4 class. Chymosin has a high specificity and it clots milk by cleavage of a single 105-Ser-Phe-|-Met-Ala-108 bond in kappa-chain of casein. An alternative name used in the art is rennin.

The term “chymosin activity” relates to chymosin activity of a chymosin enzyme as understood by the skilled person in the present context.

The skilled person knows how to determine herein relevant chymosin activity.

In working Example 4 herein is provided an example of a standard method to determine specific chymosin activity—alternatively termed clotting activity or milk clotting activity.

In working Example 5 herein is provided an example of a standard method to determine proteolytical activity,

As known in the art—the herein relevant so-called C/P ratio is determined by dividing the specific clotting activity (C) with the proteolytical activity (P).

As known in the art—a higher C/P ratio implies generally that the loss of protein during e.g. cheese manufacturing due to non-specific protein degradation is reduced, i.e. the yield of cheese is improved, and that the development of bitter taste in the cheese during maturation is reduced.

The term “isolated variant” means a variant that is modified by the hand of man. In one aspect, the variant is at least 1% pure, e.g., at least 5% pure, at least 10% pure, at least 20% pure, at least 40% pure, at least 60% pure, at least 80% pure, and at least 90% pure, as determined by SDS PAGE.

The term “mature polypeptide” means a peptide in its final form following translation and any post-translational modifications, such as N terminal processing, C terminal truncation, glycosylation, phosphorylation, etc. In the present context may a herein relevant mature chymosin polypeptide be seen as the active chymosin polypeptide sequence—i.e. without the pre-part and/or pro-part sequences. Herein relevant examples of a mature polypeptide are e.g. the mature polypeptide of SEQ ID NO: 1 (bovine chymosin), which is from amino add position 59 to amino add position 381 of SEQ ID NO: 1 or the mature polypeptide of SEQ ID NO: 2 (camel chymosin), which is from amino add position 59 to amino acid position 381 of SEQ ID NO: 2.

The term “parent” or “parent polypeptide having chymosin activity” means a polypeptide to which an alteration is made to produce the enzyme variants of the present invention. The parent may be a naturally occurring (wild-type) polypeptide or a variant thereof.

The term “Sequence identity” relates to the relatedness between two amino acid sequences or between two nucleotide sequences.

For purposes of the present invention, the degree of sequence identity between two amino acid sequences is determined using the Needleman-Wunsch algorithm (Needleman and Wunsch, 1970, J. Mol. Biol. 48: 443-453) as implemented in the Needle program of the EMBOSS package (EMBOSS: The European Molecular Biology Open Software Suite, Rice et al., 2000, Trends Genet. 16: 276-277), preferably version 3.0.0 or later. The optional parameters used are gap open penalty of 10, gap extension penalty of 0.5, and the EBLOSUM62 (EMBOSS version of BLOSUM62) substitution matrix. The output of Needle labeled “longest identity” (obtained using the -nobrief option) is used as the percent identity and is calculated as follows:

(Identical Residues×100)/(Length of Alignment Total Number of Gaps in Alignment)

For purposes of the present invention, the degree of sequence identity between two deoxyribonucleotide sequences is determined using the Needleman-Wunsch algorithm (Needleman and Wunsch, 1970, supra) as implemented in the Needle program of the EMBOSS package (EMBOSS: The European Molecular Biology Open Software Suite, Rice et al., 2000, supra), preferably version 3.0.0 or later. The optional parameters used are gap open penalty of 10, gap extension penalty of 0.5, and the EDNAFULL (EMBOSS version of NCBI NUC4.4) substitution matrix. The output of Needle labeled “longest identity” (obtained using the -nobrief option) is used as the percent identity and is calculated as follows:

(Identical Deoxyribonucleotides×10)/(Length of Alignment Total Number of Gaps in Alignment).

The term “variant” means a peptide having chymosin activity comprising an alteration, i.e., a substitution, insertion, and/or deletion, at one or more (several) positions. A substitution means a replacement of an amino acid occupying a position with a different amino acid; a deletion means removal of an amino acid occupying a position; and an insertion means adding 1-3 amino acids adjacent to an amino acid occupying a position.

The amino acid may be natural or unnatural amino acids—for instance, substitution with e.g. a particularly D-isomers (or D-forms) of e.g. D-alanine could theoretically be possible.

The term “wild-type” chymosin peptide means a chymosin expressed by a naturally occurring organism, such as a mammalian (e.g. camel or bovine) found in nature.

DRAWINGS

FIG. 1: An alignment of herein relevant different chymosin sequences. The shown “Bos_bovis_chymosin_B” is bovine chymosin SEQ ID NO: 1 herein and the shown “Camelus_dromedarius” is camel chymosin of SEQ ID NO: 2 herein, Using bovine chymosin of SEQ ID NO: 1 as reference sequence as described herein is can e.g. be seen that bovine chymosin has “V” in position 10 and camel chymosin has “A” in the same position 10. It may e.g. also be seen that bovine/Rat have “Q” in position 352 and Camel/C._bactrianus have “E” in the same position 352. FIG. 1 discloses SEQ ID NOS 1, 3, 4, 2, 5 and 6, respectively, in order of appearance.

In relation to the chymosin sequences shown in FIG. 1—sheep has 94.5% sequence identity with bovine SEQ ID NO: 1; C._bactrianus has 83.2% sequence identity with bovine SEQ ID NO: 1; Camelus_dromedarius (camel chymosin of SEQ ID NO: 2) has 84% sequence identity with bovine SEQ ID NO: 1; pig has 80.3% sequence identity with bovine SEQ ID NO: 1 and rat has 71.9% sequence with bovine identity SEQ ID NO: 1.

As understood by the skilled person in the present context—herein relevant sequence identity percentages of mature polypeptide sequences of e.q. sheep, C._bactrianus, camel, pig or rat chymosin with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin—i.e. amino acid positions 59 to 381 of SEQ ID NO: 1) are relatively similar to above mentioned sequence identity percentages.

FIG. 2: The 3D structure of bovine chymosin—the 3D structure is public available. As an example are shown where the amino acid positions 296 and 294 are present in bovine Chymosin.

DETAILED DESCRIPTION OF THE INVENTION

Determining the Amino Acid Position of a Chymosin of Interest

As discussed above—as a reference sequence for determining the amino acid position of a herein relevant chymosin polypeptide of interest (e.g. camel, sheep, bovine etc) is herein used the public known bovine chymosin sequence disclosed as SEQ ID NO: 1 herein.

For purposes of the present invention, the polypeptide disclosed in SEQ ID NO: 1 (bovine chymosin) is used to determine the corresponding amino acid residue in another chymosin polypeptide. The amino add sequence of another chymosin polypeptide is aligned with the polypeptide disclosed in SEQ ID NO: 1, and based on the alignment, the amino acid position number corresponding to any amino acid residue in the polypeptide disclosed in SEQ ID NO: 1 is determined us ng the ClustalW algorithm as described in working Example 1 herein.

Identification of the corresponding amino acid residue in another chymosin polypeptide can be confirmed by using the Needleman-Wunsch algorithm (Needleman and Wunsch, 1970, J. Mol. Biol. 48: 443-453) as implemented in the Needle program of the EMBOSS package (EMBOSS: The European Molecular Biology Open Software Suite, Rice et al., 2000, Trends Genet. 16: 276-277), preferably version 3.0.0 or later.

Based on above well known computer programs—it is routine work for the skilled person to determine the amino acid position of a herein relevant chymosin polypeptide of interest (e.g. camel, sheep, bovine etc).

In FIG. 1 herein is shown an example of an alignment.

Just as an example—in FIG. 1 can e.g. be seen that herein used bovine reference SEQ ID NO: 1 has a “G” in position 50 and “Camelus_dromedarius” (SEQ ID NO: 2 herein) has an “A” in this position 50.

Nomenclature of Variants

In describing the variants of the present invention, the nomenclature described below is adapted for ease of reference. The accepted IUPAC single letter or three letter amino acid abbreviations are employed.

The specific variants discussed in this “nomenclature” section below may not be herein relevant variants of the present invention—i.e. this “nomenclature” section is just to describe the herein relevant used nomenclature as such.

Substitutions. For an amino acid substitution, the following nomenclature is used: Original amino acid, position, substituted amino acid. Accordingly, a theoretical substitution of threonine with alanine at position 226 is designated as “Thr226Ala” or “T226A”. Multiple mutations are separated by addition marks (“+”), e.g., “Gly205Arg+Ser411Phe” or “G205R+S411F”, representing substitutions at positions 205 and 411 of glycine (G) with arginine (R) and serine (S) with phenylalanine (F), respectively. A substitution e.g. designated “226A” refers to a substitution of a parent amino acid (e.g. T, Q, S or another parent amino acid) with alanine at position 226.

Deletions. For an amino acid deletion, the following nomenclature is used: Original amino acid, position, *. Accordingly, the deletion of glycine at position 195 is designated as “Gly195*” or “G195*”. Multiple deletions are separated by addition marks (“+”), e.g., “Gly195*+Ser411*” or “G195+S411*”.

Insertions. For an amino add insertion, the following nomenclature is used: Original amino add, position, original amino acid, inserted amino acid. Accordingly the insertion of lysine after glycine at position 195 is designated “Gly195GlyLys” or “G195GK”. An insertion of multiple amino acids is designated [Original amino acid, position, original amino acid, inserted amino acid #1, inserted amino acid #2; etc.]. For example, the insertion of lysine and alanine after glycine at position 195 is indicated as “Gly195GlyLysAla” or “G195GKA”.

In such cases the inserted amino add residue(s) are numbered by the addition of lower case letters to the position number of the amino acid residue preceding the inserted amino acid residue(s). In the above example, the sequence would thus be:

Parent: Variant: 195 195 195a 195b G G - K- A

Multiple alterations. Variants comprising multiple alterations are separated by addition marks (“+”), e.g., “Arg170Tyr+Gly195Glu” or “R170Y+G195E” representing a substitution of tyrosine and glutamic acid for arginine and glycine at positions 170 and 195, respectively.

Different Substitutions. Where different substitutions can be introduced at a position, the different substitutions are separated by a comma, e.g., “Arg170Tyr,Glu” or “R170Y,E” represents a substitution of arginine with tyrosine or glutamic acid at position 170. Thus, “Tyr167Gly,Ala+Arg170Gly,Ala” or

“Y167G,A+R170G,A” designates the following variants:

“Tyr167Gly+Arg170Gly”, “Tyr167Gly+Arg170Ala”, “Tyr167Ala+Arg170Gly”, and “Tyr167Ala+Arg170Ala”.

A Method for Making an Isolated Chymosin Polypeptide Variant

As discussed above—as known in the art, the skilled person may based on his common general knowledge routinely produce and purify chymosin and chymosin variants.

Said in other words, once the skilled person is in possession of a herein relevant parent polypeptide having chymosin activity of interest (e.g. from bovines, camels, sheep, pigs, or rats) it is routine work for the skilled person to make a variant of such a parent chymosin of interest.

An example of a suitable method to produce and isolate a chymosin (variant or parent) may be by well known e.g. fungal recombinant expression/production based technology as e.g. described in WO02/6752A2 (Chr. Hansen).

It is also routine work for the skilled person to make alteration at one or more positions in a parent polypeptide having chymosin activity, wherein the alteration is comprising a substitution, a deletion or an insertion in at least one amino acid position.

As known to the skilled person—this may e.g. be done by so-called site directed mutageneis and recombinant expression/production based technology.

It is also routine work for the skilled person to determine if a herein relevant parent polypeptide (e.g. camel or bovine wildtype chymosin) and/or a herein relevant variant has chymosin activity or not.

As known in the art—chymosin activity may be determined by the so-called C/P ratio, which is determined by dividing the specific clotting activity (C) with the proteolytical activity (P).

As known in the art—a higher C/P ratio implies generally that the loss of protein during e.g. cheese manufacturing due to non-specific protein degradation is reduced, i.e. the yield of cheese is improved, and that the development of bitter taste in the cheese during maturation is reduced.

In working example 4 herein is described a suitable method to determine the specific clotting activity (C) and in working example 5 herein is described a suitable method to determine proteolytical activity (P).

Preferably, an isolated chymosin polypeptide variant as described herein is a variant, wherein the variant has a chymosin activity giving a higher C/P ratio as compared to the C/P ratio of bovine chymosin comprising the mature polypeptide of SEQ ID NO: 1 herein.

Preferably, an isolated chymosin polypeptide variant as described herein is a variant, wherein the variant has a chymosin activity giving a higher C/P ratio as compared to the C/P ratio of camel chymosin comprising the mature polypeptide of SEQ ID NO: 2 herein.

More preferably, an isolated chymosin polypeptide variant as described herein is a variant, wherein the variant has

-   -   a chymosin activity giving a higher C/P ratio as compared to the         C/P ratio of bovine chymosin comprising the mature polypeptide         of SEQ ID NO: 1 herein; and     -   a chymosin activity giving a higher C/P ratio as compared to the         C/P ratio of camel chymosin comprising the mature polypeptide of         SEQ ID NO: 2 herein.

As discussed above as a reference sequence for determining the amino acid position of a herein relevant chymosin polypeptide of interest (e.g. camel, sheep, bovine etc) is herein used the public known bovine chymosin sequence disclosed as SEQ ID NO: 1 herein.

As discussed above—based on e.g. the computer sequence alignment programs discussed herein—it is routine work for the skilled person to determine the herein relevant amino acid position of a herein relevant chymosin polypeptide of interest (e.g. camel, sheep, bovine etc).

The term “the parent polypeptide has at least 65% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin)” of e.g. the method of the first aspect herein may be seen as relating to a sequence based limitation of the parent chymosin polypeptide used to make a herein relevant variant thereof.

Said in other words—a mature parent chymosin polypeptide (e.g. sheep or pig) that has at least 65% sequence identity with the mature Bovine chymosin is believed to be sufficient structural identical to e.g. Bovine or Camel chymosin in order to be herein relevant—i.e. in the present context it is believed that a mature parent chymosin polypeptide (e.g. from e.g. sheep or rat) that has at least 65% sequence identity with the mature polypeptide SEQ ID NO: 1 (bovine chymosin) may herein be seen as sufficient structural related to e.g. bovine or camel chymosin in order to be improved by making a variant in any of the amino acid positions as described herein.

The camel chymosin polypeptide of SEQ ID NO: 2 has 84% sequence identity with the bovine polypeptide of SEQ ID NO: 1 (i.e. the complete SEQ ID NO: 1 from position 1 to 381, which includes pre and pro sequence).

As understood by the skilled person in the present context—a herein relevant parent polypeptide having chymosin activity may already e.g. be a variant of e.g. a corresponding wildtype chymosin.

For instance, a camel chymosin variant with e.g. 5-10 alterations (e.g. substitutions) as compared to wildtype camel chymosin polypeptide of SEQ ID NO: 2 will still be a parent polypeptide that has at least 65% sequence identity with the mature polypeptide of SEQ ID NO: 1 (Bovine) as required in e.g. first aspect herein.

Said in other words, a herein relevant isolated chymosin polypeptide variant may comprise alterations (e.g. substitutions) in other position than the positions of e.g. the first aspect herein.

In relation to the chymosin sequences shown in FIG. 1 herein—sheep has 94.5% sequence identity with bovine SEQ ID NO: 1; C._bactrianus has 83.2% sequence identity with bovine SEQ ID NO: 1; pig has 80.3% sequence identity with bovine SEQ ID NO: 1 and rat has 71.9% sequence with bovine identity SEQ ID NO: 1.

As understood by the skilled person m the present context—herein relevant sequence identity percentages of e.g. mature sheep, C._bactrianus, camel, pig or rat chymosin with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin—i.e. amino acid positions 59 to 381 of SEQ ID NO: 1) are relatively similar to above mentioned sequence identity percentages.

Preferred Variant:

As discussed above—e.g. the first aspect relates to an isolated chymosin polypeptide variant, wherein the alteration is comprising a substitution, a deletion or an insertion in at least one amino acid position corresponding to any of positions 117, 134, 141, 143, 156, 241, 279, 280, 281, 298, 300, 307, 309, 311, 325, 350, 352 and 353.

A preferred embodiment relates to an isolated chymosin polypeptide variant, wherein the alteration comprises a substitution, a deletion or an insertion in at least one amino add position corresponding to any of positions 134, 141, 143, 280, 281, 298, 300, 307, 309, 311, 352 and 353.

It may be preferred that at least one alteration is a substitution—i.e. a herein relevant preferred embodiment relates to an isolated chymosin polypeptide variant, wherein the alteration is comprising a substitution in at least one amino acid position corresponding to any of positions 117, 134, 141, 143, 156, 241, 279, 280, 281, 298, 300, 307, 309, 311, 325, 350, 352 and 353.

Preferably, an isolated chymosin polypeptide variant, wherein the alteration is comprising a substitution in at least one amino acid position corresponding to any of positions 134, 141, 143, 280, 281, 298, 300, 307, 309, 311, 352 and 353.

Preferably, the substitution is wherein the substitution is 117N, 134Q, 141E, 143F, 156V, 241I, 279M, 280I, 281V, 298E, 300R, 307D, 309D, 309W, 311I, 325M, 350N, 352L, 352Q, 353L or 353Q.

As understood by the skilled person in the present context—if the parent chymosin polypeptide already has e.g. “V” in position 156 then is does not make sense to talk about making the substitution 156V for this specific parent chymosin polypeptide. As can be seen in FIG. 1 herein—rat wildtype chymosin has “V” in position 156—the substitution 156V may be seen as herein irrelevant for the specific rat chymosin polypeptide sequence of FIG. 1.

Preferably, the substitution is wherein the substitution is 134Q, 141E, 143F, 280I, 281V, 298E, 300R, 307D, 309D, 309W, 311I, 352L, 352Q, 353L or 353Q.

Preferably, the substitution is wherein the substitution is D117N, H134Q, Q141E, I143E, D156V, V241I, V279M, L280I, F281V, Q298E, Q300R, N307D, G309D, G309W, L311I, D325M, H350N, Q352L, E352L, E352Q, K353L or K353Q.

As understood by the skilled person in the present context—if the parent chymosin polypeptide does not have e.g. “D” in position 156 then is does not make sense to talk about making the substitution D156V for this specific parent chymosin polypeptide. As can be seen in FIG. 1 herein—rat wildtype chymosin has “V” in position 156—the substitution D156V may therefore be seen as herein irrelevant for the specific rat chymosin polypeptide sequence of FIG. 1.

In a preferred embodiment, the substitution is wherein the substitution is H134Q, Q141E, I143F, L280I, F281V, Q298E, Q300R, N307D, G309D, G309W, L311I, Q352L, E352L, E352Q, K353L or K353Q.

In a preferred embodiment, the substitution is wherein the substitution is:

F281V+V306I+I321L;

H134Q+I154L+D216S;

V261A+V263I+G309W+L311I+Y326E;

D156V+G309D+M314L+V317I;

H134Q+L280I+G309W;

R119Q+D156V+V375L;

Y79S+R119S+H204R;

Y79S+H134Q+Y365E+V375L;

Y194I+R213Q+G309D;

Y79S+D117N+I321L;

Y185F+D325M+E352Q;

Y79S+L224V+L311I;

S132F+H134Q+M200I+M215L+G221E;

F281V+G309W+S331Y+D337E;

D156V+G309D+M314L+V317I;

G128D+L188I+Y326E;

R119S+V241I+L280I+L311I+D325M;

R119Q+S284T+T297S+V306I+G309W

K279V+V281F;

Q298E+Q300R;

H350N+Q352E+K353L;

D307N+D309G; or

Q141E+I143F.

Preferred Parent Polypeptide Having Chymosin Activity:

Preferably, the parent polypeptide has at least 70% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin), more preferably the parent polypeptide has at least 75% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin).

Just as an example—a herein suitable relevant parent polypeptide could e.g. be bovine chymosin A—as known in the art bovine chymosin A may only have one amino acid difference as compared to bovine chymosin B of SEQ ID NO: 1 herein.

As discussed above—in working examples herein were made variants using the polypeptide of SEQ ID NO: 1 (Bovine) as parent polypeptide—such variant may herein be termed bovine chymosin variants.

Accordingly, in a preferred embodiment—the parent polypeptide has at least 90% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin), more preferably the parent polypeptide has at least 95% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin) and even more preferably the parent polypeptide has at least 97% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin). It may be preferred that the parent polypeptide is the mature polypeptide of SEQ ID NO: 1 (bovine chymosin).

As understood by the skilled person in the present context—a herein relevant parent polypeptide having chymosin activity may already e.g. be a variant of e.q. a corresponding wildtype chymosin.

For instance, a bovine chymosin variant with e.g. 5-10 alterations (e.g. substitutions) as compared to mature wildtype bovine chymosin polypeptide of SEQ ID NO: 1 will still be a parent polypeptide that has at least 95% sequence identity with the mature polypeptide of SEQ ID NO: 1 (Bovine chymosin).

The mature polypeptide of SEQ ID NO: 1 (Bovine) is 323 amino acids long—accordingly, a bovine chymosin variant with e.g. 25 amino acid substitutions as compared to mature wildtype bovine chymosin polypeptide of SEQ ID NO: 1 will not be a parent polypeptide that has at least 95% sequence identity with the mature polypeptide of SEQ ID NO: 1 (Bovine chymosin).

Said in other words and in general—a herein relevant isolated chymosin polypeptide variant may comprise alterations (e.g. substitutions) in other positions than the positions of e.g. the first aspect herein.

As discussed above—in working examples herein were made variants using the polypeptide SEQ ID NO: 2 (Camel) as parent polypeptide—such variant may herein be termed camel chymosin variant.

Accordingly, in a preferred embodiment—the parent polypeptide has at least 90% sequence identity with the mature polypeptide of SEQ ID NO: 2 (Camel chymosin), more preferably the parent polypeptide has at least 95% sequence identity with the mature polypeptide of SEQ ID NO: 2 (Camel chymosin) and even more preferably the parent polypeptide has at least 97% sequence identity with the mature polypeptide of SEQ ID NO: 2 (Camel chymosin). It may be preferred that the parent polypeptide Is the mature polypeptide of SEQ ID NO: 2 (Camel chymosin).

As understood by the skilled person in the present context—a parent polypeptide that has at least 90% sequence identity with the mature polypeptide of SEQ ID NO: 2 (Camel) is still within the SEQ ID NO: 1 (Bovine) based sequence identity requirement of point (ii) of first aspect herein—i.e. it will be a parent polypeptide that has at least 65% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin).

An Isolated Variant of Bovine Chymosin:

As discussed above—in working examples herein were made variants using the polypeptide of SEQ ID NO: 1 (Bovine) as parent polypeptide such variant may herein be termed bovine chymosin variants.

As discussed above—the third aspect accordingly relates to an isolated chymosin polypeptide variant comprising:

(a): an alteration at one or more positions in a parent polypeptide having chymosin activity, wherein the alteration is comprising a substitution, a deletion or an insertion in at least one amino acid position corresponding to any of positions 117, 134, 141, 143, 156, 241, 279, 280, 281, 298, 300, 307, 309, 311, 325, 350, 352 and 353; and

(b): wherein the variant has chymosin activity;

and wherein:

(i): the amino acid position of the parent polypeptide is determined by an alignment of the parent polypeptide with the polypeptide of SEQ ID NO: 1 (bovine chymosin)—i.e. the polypeptide of SEQ ID NO: 1 is used to determine the corresponding amino add sequence in the parent polypeptide; and

(ii): the parent polypeptide has at least 90% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin), which is from amino acid position 59 to amino acid position 381 of SEQ ID NO: 1; and

(iii): the isolated variant polypeptide has less than 100% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin).

The above described definitions and preferred embodiments are also relevant for this aspect.

Preferably, an isolated bovine chymosin polypeptide variant as described herein is a variant, wherein the variant has a chymosin activity giving a higher C/P ratio as compared to the C/P ratio of bovine chymosin comprising the mature polypeptide of SEQ ID NO: 1.

In a preferred embodiment—the parent polypeptide has at least 92% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin), more preferably the parent polypeptide has at least 95% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin) and even more preferably the parent polypeptide has at least 97% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin).

As understood by the skilled person in the present context—an isolated chymosin variant may comprise alterations (e.g. substitutions) in other amino acid positions than given above.

For instance, a bovine chymosin variant with e.g. 5-10 alterations (e.g. substitutions) as compared to wildtype bovine chymosin polypeptide of SEQ ID NO: 1 will still be a parent polypeptide that has at least 95% sequence identity with the mature polypeptide of SEQ ID NO: 1 (Bovine chymosin).

It may be preferred that the isolated bovine chymosin variant comprises less than amino add alterations (e.g. substitutions) as compared to the mature polypeptide of SEQ ID NO: 1 (bovine chymosin) or it may be preferred that the isolated bovine chymosin variant comprises less than 20 amino acid alterations (e.g. substitutions) as compared to the mature polypeptide of SEQ ID NO: 1 (bovine chymosin) or it may be preferred that the isolated bovine chymosin variant comprises less than 10 amino acid alterations (e.g. substitutions) as compared to the mature polypeptide of SEQ ID NO: 1 (bovine chymosin) or it may be preferred that the isolated bovine chymosin variant comprises less than 5 amino add alterations (e.g. substitutions) as compared to the mature polypeptide of SEQ ID NO: 1 (bovine chymosin).

As understood by the skilled person in the present context—the term “the isolated variant polypeptide has less than 100% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin)” of point (iii) above relates to that the herein described isolated bovine chymosin variant shall of course not have a polypeptide sequence that is 100% identical to the public known wildtype bovine chymosin sequence of SEQ ID NO: 1.

A preferred embodiment relates to an isolated bovine chymosin polypeptide variant, wherein the alteration comprises a substitution, a deletion or an insertion in at least one amino acid position corresponding to any of positions 134, 141, 143, 280, 281, 298, 300, 307, 309, 311, 352 and 353.

It may be preferred that at least one alteration is a substitution—i.e. a herein relevant preferred embodiment relates to an isolated chymosin polypeptide variant, wherein the alteration is comprising a substitution in at least one amino acid position corresponding to any of positions 117, 134, 141, 143, 156, 241, 279, 280, 281, 298, 300, 307, 309, 311, 325, 350, 352 and 353.

Preferably, an isolated chymosin polypeptide variant, wherein the alteration is comprising a substitution in at least one amino acid position corresponding to any of positions 134, 141, 143, 280, 281, 298, 300, 307, 309, 311, 352 and 353,

Preferably, the substitution is wherein the substitution is 117N, 134Q, 141E, 143F, 156V, 241I, 279M, 280I, 281V, 298E, 300R, 307D, 309D, 309W, 311I, 325M, 350N, 352L, 352Q, 353L or 353Q.

Preferably, the substitution is wherein the substitution is 134Q, 141E, 143F, 280I, 281V, 298E, 300R, 307D, 309D, 309W, 311I, 352L, 352Q, 353L or 353Q.

Preferably, the substitution is wherein the substitution is D117N, H134Q, Q141E, I143F, D156V, V241I, V279M, L280I, F281V, Q298E, Q300R, N307D, G309D, G309W, L311I, D325M, H350N, Q352L, E352L, E352Q, K353L or K353Q.

In a preferred embodiment, the substitution is wherein the substitution is:

F281V+V306I+I321L;

H134Q+I154L+D216S;

V261A+V263I+G309W+L311I+Y326F;

D156V+G309D+M314L+V317I;

H134Q+L280I+G309W;

R119Q+D156V+V375L;

Y79S+R119S+H204R;

Y79S+H134Q+Y365F+V375L;

V194I+R213Q+G309D;

Y79S+D117N+I321L;

Y185F+D325M+E352Q;

Y79S+L224V+L311I;

S132F+H134Q+M200I+M215L+G221E;

F281V+G309W+S331Y+D337E;

D156V+G309D+M314L+V317I;

G128D+L188I+Y326F;

R119S+V241I+L280I+L311I+D325M;

R119Q+S284T+T297S+V306I+G309W

K279V+V281F;

Q298E+Q300R;

H350N+Q352E+K353L;

D307N+D309G; or

Q141E+I143F.

An Isolated Variant of Camel Chymosin:

As discussed above—in working examples herein were made variants using the polypeptide of SEQ ID NO: 2 (camel chymosin) as parent polypeptide—such variant may herein be termed camel chymosin variant.

As discussed above—the fourth aspect accordingly relates to an isolated chymosin polypeptide variant comprising:

(a): an alteration at one or more positions in a parent polypeptide having chymosin activity, wherein the alteration is comprising a substitution, a deletion or an insertion in at least one amino acid position corresponding to any of positions 117, 134, 141, 143, 156, 241, 279, 280, 281, 298, 300, 307, 309, 311, 325, 350, 352 and 353; and

(b): wherein the variant has chymosin activity;

and wherein:

(i): the amino add position of the parent polypeptide is determined by an alignment of the parent polypeptide with the polypeptide of SEQ ID NO: 1 (bovine chymosin)—i.e. the polypeptide of SEQ ID NO: 1 is used to determine the corresponding amino acid sequence in the parent polypeptide; and

(ii): the parent polypeptide has at least 90% sequence identity with the mature polypeptide of SEQ ID NO: 2 (camel chymosin); and

(iii): the isolated variant polypeptide has less than 100% sequence identity with the mature polypeptide of SEQ ID NO: 2 (camel chymosin).

The above described definitions and preferred embodiments are also relevant for this aspect.

Preferably, an isolated camel chymosin polypeptide variant as described herein is a variant, wherein the variant has a chymosin activity giving a higher C/P ratio as compared to the C/P ratio of camel chymosin comprising the mature polypeptide of SEQ ID NO: 2.

In a preferred embodiment—the parent polypeptide has at least 92% sequence identity with the mature polypeptide of SEQ ID NO: 2 (camel chymosin), more preferably the parent polypeptide has at least 95% sequence identity with the mature polypeptide of SEQ ID NO: 2 (camel chymosin) and even more preferably the parent polypeptide has at least 97% sequence identity with the mature polypeptide of SEQ ID NO: 2 (camel chymosin).

As understood by the skilled person in the present context—an isolated chymosin variant may comprise alterations (e.g. substitutions) in other amino acid positions than given above.

For instance, a camel chymosin variant with e.g. 5-10 alterations (e.g. substitutions) as compared to wildtype camel chymosin polypeptide of SEQ ID NO: 2 will still be a parent polypeptide that has at least 95% sequence identity with the mature polypeptide of SEQ ID NO: 2 (camel chymosin).

It may be preferred that the isolated camel chymosin variant comprises less than 30 amino acid alterations (e.g. substitutions) as compared to the mature polypeptide of SEQ ID NO: 2 (camel chymosin) or it may be preferred that the isolated camel chymosin variant comprises less than 20 amino acid alterations (e.g. substitutions) as compared to the mature polypeptide of SEQ ID NO: 2 (camel chymosin) or it may be preferred that the isolated camel chymosin variant comprises less than 10 amino acid alterations (e.g. substitutions) as compared to the mature polypeptide of SEQ ID NO: 2 (camel chymosin) or it may he preferred that the isolated camel chymosin variant comprises less than 5 amino acid alterations (e.g. substitutions) as compared to the mature polypeptide of SEQ ID NO: 2 (camel chymosin).

As understood by the skilled person in the present context—the term “the isolated variant polypeptide has less than 100% sequence identity with the mature polypeptide of SEQ ID NO: 2 (camel chymosin)” of point (iii) above relates to that the herein described isolated camel chymosin variant shall of course not have a polypeptide sequence that is 100% identical to the public known wildtype camel chymosin sequence of SEQ ID NO: 2.

A preferred embodiment relates to an isolated camel chymosin polypeptide variant, wherein the alteration comprises a substitution, a deletion or an insertion in at least one amino acid position corresponding to any of positions 134, 141, 143, 280, 281, 298, 300, 307, 309, 311, 352 and 353.

It may be preferred that at least one alteration is a substitution—i.e. a herein relevant preferred embodiment relates to an isolated chymosin polypeptide variant, wherein the alteration is comprising a substitution in at least one amino acid position corresponding to any of positions 117, 134, 141, 143, 156, 241, 279, 280, 281, 298, 300, 307, 309, 311, 325, 350, 352 and 353.

Preferably, an isolated chymosin polypeptide variant, wherein the alteration is comprising a substitution in at least one amino acid position corresponding to any of positions 134, 141, 143, 280, 281, 298, 300, 307, 309, 311, 352 and 353.

Preferably, the substitution is wherein the substitution is 117N, 134Q, 141E, 143E, 156V, 241I, 279M, 280I, 281V, 298E, 300R, 307D, 309D, 309W, 311I, 325M, 350N, 352L, 352Q, 353L or 353Q.

Preferably, the substitution is wherein the substitution is 134Q, 141E, 143F, 280I, 281V, 298E, 300R, 307D, 309D, 309W, 311I, 352L, 352Q, 353L or 353Q.

Preferably, the substitution is wherein the substitution is D117N, H134Q, Q141E, I143F, D156V, V241I, V279M, L280I, F281 V, Q298E, Q300R, N307D, G309D, G309W, L311I, D325M, H350N, Q352L, E352L, E352Q, K353L or K353Q.

In a preferred embodiment, the substitution is wherein the substitution is:

F281V+V306I+I321L;

H134Q+I154L+D216S;

V261A+V263I+G309W+L311I+Y326F;

D156V+G309D+M314L+V317I;

H134Q+L280I+G309W;

R119Q+D156V+V375L;

Y79S+R119S+H204R;

Y79S+H134Q+Y365F+V375L;

Y194I+R213Q+G309D;

Y79S+D117N+I321L;

Y185F+D325M+E352Q;

Y79S+L224V+L311I;

S132F+H134Q+M200I+M215L+G221E;

F281V+G309W+S331Y+D337E;

D156V+G309D+M314L+V317I;

G128D+L188I+Y326F;

R119S+V241I+L280I+L311I+D325M;

R119Q+S284T+T297S+V306I+G309W

K279V+V281F;

Q298E+Q300R;

H350N+Q352E+K353L;

D307N+D309G; or

Q141E+I143F.

A Method for Making a Milk Based Product

As discussed above—an isolated chymosin polypeptide variant as described herein may be used according to the art—e.g. to make a milk based product of interest (such as e.g. a cheese product).

As discussed above—an aspect of the invention relates to a method for making a food or feed product comprising adding en effective amount of the isolated chymosin polypeptide variant as described herein to the food or feed ingredient(s) and carrying our further manufacturing steps to obtain the food or feed product.

Preferably, the food or feed product is a milk based product and wherein the method comprises adding an effective amount of the isolated chymosin polypeptide variant as described herein to milk and carrying our further manufacturing steps to obtain the milk based product.

The milk may e.g. be soy milk, sheep milk, goat milk, buffalo milk, yak milk, lama milk, camel milk or cow milk.

The milk based product may e.g. be a fermeneted milk product, a quark or a cheese.

Aspects/Embodiments Herein—Presented in Claim Format

Herein described aspects and preferred embodiments of the invention may be presented/described in a so-called claim format—this is done below.

1. A method for making an isolated chymosin polypeptide: variant comprising the steps:

(a): making an alteration at one or more positions in a parent polypeptide having chymosin activity, wherein the alteration is comprising a substitution, a deletion or an insertion in at least one amino add position corresponding to any of positions 117, 134, 141, 143, 156, 241, 279, 280, 281, 298, 300, 307, 309, 311, 325, 350, 352 and 353; and

(b): producing and isolating the altered polypeptide of step (a) and thereby obtaining the isolated chymosin polypeptide variant, wherein the variant has chymosin activity;

and wherein:

(i): the amino acid position of the parent polypeptide is determined by an alignment of the parent polypeptide with the polypeptide of SEQ ID NO: 1 (bovine chymosin)—i.e. the polypeptide of SEQ ID NO: 1 is used to determine the corresponding amino acid sequence in the parent polypeptide; and

(ii): the parent polypeptide has at least 65% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin), which is from amino acid position 59 to amino acid position 381 of SEQ ID NO: 1.

2. The method for making an isolated chymosin polypeptide variant of claim 1, wherein the isolated chymosin polypeptide variant has:

-   -   a chymosin activity giving a higher C/P ratio as compared to the         C/P ratio of bovine chymosin comprising the mature polypeptide         of SEQ ID NO: 1; and

a chymosin activity giving a higher C/P ratio as compared to the C/P ratio of camel chymosin comprising the mature polypeptide of SEQ ID NO: 2.

3. The method for making an isolated chymosin polypeptide variant of any of the preceding claims, wherein the alteration comprises a substitution, a deletion or an insertion in at least one amino acid position corresponding to any of positions 134, 141, 143, 280, 281, 298, 300, 307, 309, 311, 352 and 353.

4. The method for making an isolated chymosin polypeptide variant of any of the preceding claims, wherein the alteration is comprising a substitution in at least one amino acid position corresponding to any of positions 117, 134, 141, 143, 156, 241, 279, 280, 281, 298, 300, 307, 309, 311, 325, 350, 352 and 353.

5. The method for making an isolated chymosin polypeptide variant of any of the preceding claims, wherein the alteration is comprising a substitution in at least one amino acid position corresponding to any of positions 134, 141, 143, 280, 281, 298, 300, 307, 309, 311, 352 and 353.

6. The method for making an isolated chymosin polypeptide variant of claim 4, wherein the substitution is 117N, 134Q, 141E, 143E, 156V, 241I, 279M, 280I, 281V, 298E, 300R, 307D, 309D, 309W, 311I, 325M, 350N, 352L, 352Q, 353L or 353Q.

7. The method for making an isolated chymosin polypeptide variant of claim 6, wherein the substitution is 134Q, 141E, 143F, 280I, 281V, 298E, 300R, 307D, 309D, 309W, 311I, 352L, 352Q, 353L or 353Q.

8. The method for making an isolated chymosin polypeptide variant of claim 4, wherein the substitution is D117N, H134Q, Q141E, I143F, D156V, V241I, V279M, L280I, F281V, Q298E, Q300R, N307D, G309D, G309W, L311I, D325M, H350N, Q352L, E352L, E352Q, K353L or K353Q.

9. The method for making an isolated chymosin polypeptide variant of claim 8, wherein the substitution is H134Q, Q141E, I143F, L280I, F281V, Q298E, Q300R, N307D, G309D, G309W, L311I, Q352L, E352L, E352Q, K353L or K353Q.

10. The method for making an isolated chymosin polypeptide variant of claim 4, wherein the substitution is:

F281V+V306I+I321L;

H134Q+I154L+D215S;

V261A+V263I+G309W+L311I+Y326F;

D156V+G309D+M314L+V317I;

H134Q+L280I+G309W

R119Q+D156V+V375L;

Y79S+R119S+H204R;

Y79S+H134Q+Y365F+V375L;

Y194I+R213Q+G309D;

Y79S+D117N+I321L;

Y185F+D325M+E352Q;

Y79S+L224V+L311I;

S132F+H134Q+M200I+M215L+G221E;

F281V+G309W+S331Y+D337E;

D156V+G309D+314L+V317I;

G128D+L188I+Y326F;

R119S+V241I+L280I+L311I+D325M;

R119Q+S284T+T297S+V306I+G309W

K279V+V281F;

Q298E+Q300R;

H350N+Q352E+K353L;

D307N+D309G; or

Q141E+I143F.

11. The method for making an isolated chymosin polypeptide variant of any of the preceding claims, wherein the parent polypeptide has at least 75% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin).

12. The method for making an isolated chymosin polypeptide variant of claim 11, wherein the parent polypeptide has at least 95% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin).

13. The method for making an isolated chymosin polypeptide variant of any of claims 1 to 10, wherein the parent polypeptide has at least 95% sequence identity with the mature polypeptide of SEQ ID NO: 2 (Camel chymosin), which is from amino acid position 59 to amino acid position 381 of SEQ ID NO: 2.

14. An isolated chymosin polypeptide variant obtained by the method of any of claims 1 to 13.

15. An isolated chymosin polypeptide variant comprising:

(a): an alteration at one or more positions in a parent polypeptide having chymosin activity, wherein the alteration is comprising a substitution, a deletion or an insertion in at least one amino acid position corresponding to any of positions 117, 134, 141, 143, 156, 241, 279, 280, 281, 298, 300, 307, 309, 311, 325, 350, 352 and 353; and

(b): wherein the variant has chymosin activity;

and wherein:

(i): the amino acid position of the parent polypeptide is determined by an alignment of the parent polypeptide with the polypeptide of SEQ ID NO: 1 (bovine chymosin)—i.e. the polypeptide of SEQ ID NO: 1 is used to determine the corresponding amino add sequence in the parent polypeptide; and

(ii): the parent polypeptide has at least 90% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin), which is from amino acid position 59 to amino acid position 381 of SEQ ID NO: 1; and

(iii): the isolated variant polypeptide has less than 100% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin).

16. The isolated chymosin polypeptide variant of claim 15, wherein the isolated variant has a chymosin activity giving a higher C/P ratio as compared to the C/P ratio of bovine chymosin comprising the mature polypeptide of SEQ ID NO: 1.

17. The isolated chymosin polypeptide variant of any of claims 15 to 16, wherein the parent polypeptide has at least 97% sequence identity with the mature polypeptide of SEQ ID NO: 1 (bovine chymosin).

18. The isolated chymosin polypeptide variant of any of claims 15 to 17, wherein the isolated bovine chymosin variant comprises less than 10 amino acid alterations (e.g. substitutions) as compared to the mature polypeptide of SEQ ID NO: 1 (bovine chymosin).

19. The isolated chymosin polypeptide variant of any of claims 15 to 18, wherein the alteration comprises a substitution, a deletion or an insertion in at least one amino acid position corresponding to any of positions 134, 141, 143, 280, 281, 298, 300, 307, 309, 311, 352 and 353.

20. The isolated chymosin polypeptide variant of any of claims 15 to 19, wherein the alteration is comprising a substitution in at least one amino acid position corresponding to any of positions 117, 134, 141, 143, 156, 241, 279, 280, 281, 298, 300, 307, 309, 311, 325, 350, 352 and 353.

21. The isolated chymosin polypeptide variant of claim 20, wherein the alteration is comprising a substitution in at least one amino acid position corresponding to any of positions 134, 141, 143, 280, 281, 298, 300, 307, 309, 311, 352 and 353.

22. The isolated chymosin polypeptide variant of claim 20, wherein the substitution is 117N, 134Q, 141E, 143F, 156V, 241I, 279M, 280I, 281V, 298E, 300R, 307D, 309D, 309W, 311I, 325M, 350N, 352L, 352Q, 353L or 353Q.

23. The isolated chymosin polypeptide variant of claim 22, wherein the substitution is 134Q, 141E, 143F, 280I, 281V, 298E, 300R, 307D, 309D, 309W, 311I, 352L, 352Q, 353L or 353Q.

24. The isolated chymosin polypeptide variant of claim 22, wherein the substitution is D117N, H134Q, Q141E, I143F, D156V, V241I, V279M, L280I, F281V, Q298E, Q300R, N307D, G309D, G309W, L311I, D325M, H350N, Q352L, E352L, E352Q, K353L or K353Q.

25. The isolated chymosin polypeptide variant of claim 20, wherein the substitution is:

F281V+V306I+I321L;

H134Q+I154L+D216S;

V261A+V263I+G309W+L311I+Y326F;

D156V+G309D+M314L+V317I;

H134Q+L280I+G309W;

R119Q+D156V+V375L;

Y79S+R119S+H204R;

Y79S+H134Q+Y365F+V375L;

Y194I+R213Q+G309D;

Y79S+D117N+I321L;

Y185F+D325M+E352Q;

Y79S+L224V+L311I;

S132F+H134Q+M200I+M215L+G221E;

F281V+G309W+S331Y+D337E;

D156V+G309D+M314L+V317I;

G128D+L188I+Y326F;

R119S+V241I+L280I+L311I+D325M;

R119Q+S284T+T297S+V306I+G309W

K279V+V281F;

Q298E+Q300 R;

H350N+Q352E+K353L;

D307N+D309G; or

Q141E+I143F,

26. An isolated chymosin polypeptide variant comprising

(a): an alteration at one or more positions in a parent polypeptide having chymosin activity, wherein the alteration is comprising a substitution, a deletion or an insertion in at least one amino acid position corresponding to any of positions 117, 134, 141, 143 156, 241, 279, 280, 281, 298, 300, 307, 309, 311, 325, 350, 352 and 353; and

(b): wherein the variant has chymosin activity;

and wherein:

(i): the amino acid position of the parent polypeptide is determined by an alignment of the parent polypeptide with the polypeptide of SEQ ID NO: 1 (bovine chymosin)—i.e. the polypeptide of SEQ ID NO: 1 is used to determine the corresponding amino acid sequence in the parent polypeptide; and

(ii): the parent polypeptide has at least 90% sequence identity with the mature polypeptide of SEQ ID NO: 2 (Camel chymosin), which is from amino acid position 59 to amino acid position 381 of SEQ ID NO: 2; and

(iii): the isolated variant polypeptide has less than 100% sequence identity with the mature polypeptide of SEQ ID NO: 2 (camel chymosin).

27. The isolated chymosin polypeptide variant of claim 26, wherein the isolated variant has a chymosin activity giving a higher C/P ratio as compared to the C/P ratio of camel chymosin comprising the mature polypeptide of SEQ ID NO: 2.

28. The isolated chymosin polypeptide variant of any of claims 26 to 27, wherein the parent polypeptide has at least 97% sequence identity with the mature polypeptide of SEQ ID NO: 2 (camel chymosin).

29. The isolated chymosin polypeptide variant of any of claims 26 to 28, wherein the isolated camel chymosin variant comprises less than 10 amino acid alterations (e.g. substitutions) as compared to the mature polypeptide of SEQ ID NO: 2 (camel chymosin).

30. The isolated chymosin polypeptide variant of any of claims 26 to 29, wherein the alteration comprises a substitution, a deletion or an insertion in at least one amino add position corresponding to any of positions 134, 141, 143, 280, 281, 298, 300, 307, 309, 311, 352 and 353.

31. The isolated chymosin polypeptide variant of any of claims 26 to 30, wherein the alteration is comprising a substitution in at least one amino acid position corresponding to any of positions 117, 134, 141, 143, 156, 241, 279, 280, 281, 298, 300, 307, 309, 311, 325, 350, 352 and 351.

32. The isolated chymosin polypeptide variant of claim 31, wherein the alteration is comprising a substitution in at least one amino add position corresponding to any of positions 134, 141, 143, 280, 281, 298, 300, 307, 309, 311, 352 and 353.

33. The isolated chymosin polypeptide variant of claim 31, wherein the substitution is 117N, 134Q, 141E, 143F, 156V, 241I, 279M, 280I, 281V, 298E, 300R, 307D, 309D, 309W, 311I, 325M, 350N, 352L, 352Q, 353L or 353Q.

34. The isolated chymosin polypeptide variant of claim 33, wherein the substitution is 134Q, 141E, 143F, 280I, 281V, 298E, 300R, 307D, 309D, 309W, 311I, 352L, 352Q, 353L or 353Q.

35. The isolated chymosin polypeptide variant of claim 33, wherein the substitution is D117N, H134Q, Q141 E, 1143F, D156V, V241I, V279M, L280I, F281V, Q298E, Q300R, N307D, G309D, G309W, L311I, D325M, H350N, Q352L, E352L, E352Q, K353L or K353Q.

36. The isolated chymosin polypeptide variant of claim 31, wherein the substitution is:

F281V+V306I+I321L;

H134Q+D216S;

V261A+V263I+G309W+L311I+Y326F;

D156V+G309D+M314L+V317I;

H134Q+L280I+G309W;

R119Q+D156V+V375L;

Y79S+R119S+H204R;

Y79S+H134Q+Y365F+V375L;

Y194I+R213Q+G309D;

Y79S+D117N+I321L;

Y185F+D325M+E352Q;

Y79S+L224V+L311I;

S132F+H134Q+M200I+M215L+G221E;

F281V+G309W+S331Y+D337E;

D156V+G309D+M314L+V317I;

G128D+L188I+Y326F;

R119S+V241I+L280I+L311I+D325M;

R119Q+S284T+T297S+V306I+G309W

K279V+V281F;

Q296E+Q300R;

H350N+Q352E+K353L;

D307N+D309G; or

Q141E+I143F.

37: A method for making a food or feed product comprising adding an effective amount of the isolated chymosin polypeptide variant according to any of claims 14 to 36 to the food or feed ingredient(s) and carrying our further manufacturing steps to obtain the food or feed product.

38: The method for making a food or feed product of claim 37, wherein the product is a milk based product and wherein the method comprises adding an effective amount of the isolated chymosin polypeptide variant according to any of claims 14 to 36 to milk and carrying our further manufacturing steps to obtain the milk based product.

39: The method for making a milk based product of claim 38, wherein the milk is soy milk, sheep milk, goat milk, buffalo milk, yak milk, lama milk, camel milk or cow milk.

40: The method for making a milk based product of any of claims 38 to 39, wherein the milk based product is a fermented milk product, a quark or a cheese.

EXAMPLES Example 1 Alignment and Numbering of Chymosin Protein Sequences and Variant Sequences

Chymosin protein sequences were aligned using the ClustalW algorithm as provided by the EBI (EBI, tools, multiple sequence alignment, CLUSTALW″, http://www.ebi.ac.uk/Tools/msa/clustalw2/) and as described in Larkin M A, Blackshields G, Brown N P, Chenna R, McGettigan P A, McWilliam H, Valentin F, Wallace I M, Wilm A, Lopez R, Thompson J D, Gibson T J, Higgins D G (2007). Bioinformatics 23(21), 2947-2948.

ClustalW2 settings for multiple sequence alignments were Protein weight Matrix=BLOSUM, GAP open=10, GAP EXTENSION=0.05, GAP DISTANCES=8, No End Gaps, ITERATION=none, NUMITER=1, CLUSTERING=NJ

As a reference sequence the bovine chymosin B preprochymosin was used (Genbank accession number P00794—disclosed herein as SEQ ID NO: 1), where the N-terminal Methionin has number 1 (MRCL . . . ) and the C-terminal isoleucin (in the protein sequence . . . LAKAI) has number 381. Variants were aligned against the bovine B pre-pro-chymosin and residues were numbered according to the corresponding bovine chymosin residue.

Example 2 Design of Chymosin Variants

Chymosin variants were designed using different strategies.

When there is referred to camel chymosin there is referred to camel chymosin comprising the polypeptide of SEQ ID NO: 2 herein.

Camel chymosin of SEQ ID NO: 2 may be seen as a herein relevant parent polypeptide having chymosin activity used to make camel chymosin variants thereof.

When there is referred to bovine chymosin there is referred to bovine chymosin comprising the polypeptide of SEQ ID NO: 1 herein.

Bovine chymosin of SEQ ID NO: 1 may be seen as a herein relevant parent polypeptide having chymosin activity used to make bovine chymosin variants thereof.

Variants of camel chymosin were designed based on an alignment of a large set of public known aspartic protease sequences having an identity of 25% or more compared to bovine chymosin B.

Variations were generally introduced in hypervariable regions, while conserved regions were not changed, Multiple variations were introduced in each variant construct, ensuring that each single mutation was present in multiple variant constructs (for discussion of results see example 6 below).

Variants of bovine chymosin were designed based on a comparison of bovine and camel chymosin, Bovine residues were e.g. changed to the camel counterpart (for discussion of results—see example 7 below).

Example 3 Preparation of Chymosin Variant Enzyme Material

All chymosin variants were synthesized as synthetic genes and cloned into a fungal expression vector corresponding essentially to pGAMpR-C (described in WO02/36752A2)

The vectors were transformed into E. coli and plasmid DNA was purified using standard molecular biology protocols, known to the person skilled in the art.

The variant plasmids were individually transformed into an Aspergillus niger strain and protein was produced essentially as described in WO02/36752A2 and purified using standard chromatography techniques.

As known in the art the skilled person may based on his common general knowledge produce and purify chymosin and chymosin variants—such as herein described bovine and camel chymosin variants.

Example 4 Determination of Specific Chymosin Activity

4.1 Determination of Clotting Activity

Milk clotting activity was determined using the REMCAT method, which is the standard method developed by the International Dairy Federation (IDF method).

Milk clotting activity is determined from the time needed for a visible flocculation of a standard milk substrate prepared from a low-heat, low fat milk powder with a calcium chloride solution of 0.5 q per litre (pH ≈6.5). The clotting time of a rennet sample is compared to that of a reference standard having known milk-clotting activity and having the same enzyme composition by IDE Standard 110B as the sample. Samples and reference standards were measured under identical chemical and physical conditions. Variant samples were adjusted to approximately 3 IMCU/ml using an 84 mM acetic acid pH 5.5 buffer. Hereafter, 200 μl enzyme was added to 10 ml preheated milk (32° C.) in a glass test tube placed in a water bath, capable of maintaining a constant temperature of 32° C.±1° C. under constant stirring.

The total milk dotting activity (strength) of a rennet was calculated in International Milk-Clotting Units (IMCU) per ml relative to a standard having the same enzyme composition as the sample according to the formula:

${{Strength}\mspace{14mu} {in}\mspace{14mu} {IMCU}\text{/}{ml}} = \frac{S\; {standard} \times T\; {standard} \times D\; {sample}}{D\; {standard} \times T\; {sample}}$

-   -   Standard: The milk-clotting activity of the international         reference standard for rennet.     -   Tstandard: Clotting time in seconds obtained for the standard         dilution.     -   Dsample: Dilution factor for the sample     -   Dstandard: Dilution factor for the standard     -   Tsample: Clotting time in seconds obtained for the diluted         rennet sample from addition of enzyme to time of flocculation

4.2 Determination of Total Protein Content

Total protein content was determined using the Pierce BCA Protein Assay Kit from. Thermo Scientific following the instructions of the providers.

4.3 Calculation of Specific Clotting Activity

Specific dotting activity (IMCU/mg total protein) was determined by dividing the dotting activity (IMCU/ml) by the total protein content (mg total protein per ml).

Example 5 Determination of Proteolytic Activity

General proteolytic activity was measured using fluoresecently labelled Bodipy-FL casein as a substrate (EnzChek; Molecular Bioprobes, E6638). Casein derivatives heavily labeled with pal insensitive green-fluorescent Bodipy-FL result in almost complete quenching of the conjugate's fluorescence. Protease catalyzed hydrolysis releases fluorescent Bodipy-FL. This method is very sensitive which was essential for this experiment as CHYMAX M has the lowest general proteolytical activity of all coagulants known to date.

The assay was conducted in a 0.2 M phosphate buffer adjusted to the desired pH at a final substrate concentration of 0.04 mg/ml. Prior to mixing 1 part of substrate with 1 part of enzyme, both prepared in the phosphate buffer, all enzyme variants where normalized to 50 IMCU/ml (according to Example 4). The substrate and enzyme were mixed in a 96-well Nunc Fluoro microtitter plates, sealed and incubated at 32° C. for 60 min. After incubation the sealing was removed and the fluorescence recorded in a fluorimeter.

Example 6 Evaluation of Camel Chymosin Variants

For all variants the specific clotting activity (IMCU/mg of total protein) was determined at pH 6.5 according to Example 4. The variants were ranked using the following strategy. The variant with the lowest specific activity got one point, the second lowest two points etc.

The same ranking strategy was done for the C/P ratio. The C/P ratio was determined for all variant at pH 6.5 by dividing the specific dotting activity (IMCU/mg) with the proteolytical activity.

The total points for each variant using both ranking strategies were determined and a final ranking was done, based on the sum of the points.

As a reference a camel wildtype gene and a bovine wildtype gene were included.

H05-3 42453 F281V V306I I321L x x 213 G01-1 42419 H134Q I154L D216S x x 210 G10-2 42492 V261A V263I G309W L311I Y326F 204 A09-2 42478 D156V G309D M314L V317I x 203 E01-1 42416 H134Q L280I G309W x x 200 G03-2 42436 R119Q D156V V375L x x 197 B06-2 42455 Y79S R119S H204R x x 195 B09-2 42479 Y79S H134Q Y365F V375L x 194 G02-1 42427 Y194I R213Q G309D x x 194 G04-1 42444 Y79S D117N I321L x x 193 H02-1 42428 Y185F D325M E352Q x x 189 A04-2 42438 Y79S L224V L311I x x 186 H10-2 42493 S132F H134Q M200I M215L G221E 186 H08-1 42477 F281V G309W S331Y D337E x 185 A09-2 42478 D156V G309D M314L V317I x 184 H01-1 42420 G128D L188I Y326F x x 182 G11-1 42500 R119S V241I L280I L311I D325M 181 H11-2 42501 R119Q S284T T297S V306I G309W 178 Camel 42404 x x x x x 174 G08-2 42476 Q246E G309D S329P D337E x 174 G06-1 42460 D156V M215L V241I x x 170 H09-1 42485 R125Q G128N H204R Q246E S284T 168 H07-2 42469 D117N V263I L280I V306I x 167 E06-2 42458 G128D T244S L311I x x 151 C03-2 42431 V90L I154L S335N x x 148 B07-1 42463 V194I V279M L280I S284T x 147 A03-2 42429 Y185F R213Q Q246E x x 146 E05-2 42450 D117N S329P T342S x x 145 H06-2 42461 G128N R312S S313Y Y326F x 145 B03-2 42430 R125Q V279M M314L x x 143 B10-1 42487 D216S L224V V263I F281V G309D 143 F01-1 42417 V90L R119Q H204R x x 143 E03-3 42433 H134Q K289N G302D x x 142 A02-2 42421 I154L G221E V279M x x 136 F07-2 42467 T297S I321L D325M T342S x 135 C11-2 42496 G128D I154L I258V D325M D337E 132 D02-1 42424 V261A S331Y L353K x x 132 A04-2 42438 Y79S L224V L311I x x 131 B01-1 42413 N108K L280I S313Y x x 131 D12-1 42506 S190A V279M S313Y S331Y V375L 130 A09-2 42478 D156V G309D M314L V317I x 129 F09-1 42483 V90L E352Q R374L V375L x 129 B12-1 42504 N108K D117N M215L H314L G347S 128 D11-1 42497 D156V H204R V261A I321L S329P 128 F06-2 42459 D117N V261A R312S x x 125 H12-1 42502 V90L L188I R203Q L280I D337E 124 D04-2 42441 L188I G221E Y365F x x 123 E07-2 42466 R119Q V279K K289N D325M x 123 C02-2 42423 R119S R125Q K289N x x 122 D05-1 42449 R119S L224V T297S x x 122 C08-1 42472 F281V K289N L311I S313Y x 117 B02-1 42422 S132F S180A R203Q x x 115 The term “X” denotes no change - i.e. no mutation.

As all variants included multiple mutations, the data of the ranked variants were investigated in more details using statistical methods and 3D structure analysis, to determine the individual amino add changes that have a positive or negative effect. In this investigation were also evaluated/included the bovine variants discussed in Example 7 below.

The following mutations were identified:

D117N + + Backbone lobe H134Q + + Exposed lobe L280I + + In cleft D156V + Backbone V241I + Backbone D325M + Backbone R374L — Backbone K289N — Other side flap V279K — In cleft G302D — Flap L353K — Cleft entrance L311I + + Bottom of cleft G309W + Outside small lobe G309D + V279M + The term ″+″ refers to a positive amino acid exchange - i.e. ″+ +″ is more positive than ″+″. The term ″−″ refers to a negative amino acid exchange - i.e. ″− −″ is more negative than ″−″.

The descriptions of the right column of the table relates to where the individual mutations are situated in the 3D structure of bovine chymosin. The 3D structure of bovine chymosin is publicly available. As an example are in FIG. 2 shown where the amino acid positions 296 and 294 are present in bovine Chymosin.

Conclusions

The results above demonstrate that following mutations n camel chymosin were positive (i.e. with improved C/P ratio as compared to camel wildtype chymosin):

D117N

H134Q

L280I

D156V

V241I

D325M

L311I

G309W

G309D

V279M

Example 7 Evaluation of Bovine Chymosin Variants

Bovine chymosin variants were evaluated based on their C/P ratio at pH 6.5 only.

Mutations Bovine−> Proteolytical/ Clotting/ camel IMCU mg C/P 3 K279V, V281F 127.237 37 0, 3 4 Q298E, Q300R 59.942 241 4, 0 6 H350N, Q352E, K353L 106.417 191 1, 8 7 D307N, D309G 56.349 47 0, 8 8 Q141E, I143F 91.011 176 1, 9 Bovine None 124.237 157 1, 3 (3327) Camel None 53.354 197 3, 7 (A01)

As all variants included multiple mutations and the data of the ranked variants were investigated in more details, using statistical methods and 3D structure analysis, to determine the individual amino acid changes that have a positive or negative effect. In this investigation were also evaluated/included the camel variants discussed in Example 6.

The following positive mutations for bovine chymosin were identified:

Q298E + + Q300R + + H350N + K353L + Q141E + I143F + The term ″+″ refers to a positive amino acid exchange - i.e. ″+ +″ is more positive than ″+″. The term ″−″ refers to a negative amino acid exchange - i.e. ″− −″ is more negative than ″−″.

Conclusions:

The results above demonstrate that following mutations in bovine chymosin were positive (i.e. with improved C/P ratio as compared to bovine wildtype chymosin):

Q300R

H350N

K353L

Q141E

I143F

Example 8 Positions for Making Positive Mutation in Chymosin

A comparative evaluation of the results described in examples 6 and 7 results in following data.

Catalytical cleft region 279-281

As shown in example 7, the double mutation K279V and V261F in bovine chymosin resulted in a negative effect on the C/P ratio. In camel chymosin the mutation V279K also resulted in a negative result (example 6). Therefore it is conclude that the optimal amino acid at position 281 is a V. It was also observed that the L280I mutation in camel had a positive effect

Small lobe region 298-300

As shown in example 7, the double mutation Q298E and Q300R in bovine chymosin had a positive effect on the C/P ratio.

Catalytical cleft region 350-353

As shown in example 7, the triple mutation H350N, Q352E and K353L in bovine chymosin had a positive effect on the C/P ratio.

In camel chymosin it was observed (example 5) that a L353Q had a positive effect while a L353K had a negative effect.

Small lobe region 307-311

As shown in example 7, the double mutation D307N and D309G in bovine chymosin had a negative effect on the C/P ratio.

In camel chymosin G309D and G309W have a positive effect. This implies that the D307N mutation in bovine chymosin is responsible for the negative effect in camel chymosin a L311I mutation was shown to have beneficial effects.

Back bone region 134-143

As shown in example 7, the double mutation Q141E and I143F bovine chymosin had a positive effect on the C/P ratio

Changing H134 into Q in camel chymosin was shown to have a beneficial effect

Preferred Position amino acids 280 I 281 V 298 E 300 R 352 Q (less preferred L) 309 D or W 307 D 141 E 143 F 353 Q 352 Q 311 I 134 Q

REFERENCES

1: WO02/36752A2 (Chr. Hansen)

2: Suzuki et al: Site directed mutagenesis reveals functional contribution of Thr218, Lys220 and Asp304 in chymosin, Protein Engineering, vol. 4, January 1990, pages 69-71

3: Suzuki et al: Alteration of catalytic properties of chymosin by site-directed mutagenesis, Protein Engineering, vol. 2, May 1989, pages 563-569

4: van den Brink et al: Increased production of chymosin by glycosylation, Journal of biotechnology, vol. 125, September 2006, pages 304-310.

5: Pitts et al: Expression and characterisation of chymosin pH optima mutants produced in Tricoderma reesei, Journal of Biotechnology, vol. 28, March 1993, pages 69-83

6: M. G. Williams et al: Mutagenesis, biochemical characterization and X-ray structural analysis of point mutants of bovine chymosin, Protein engineering design and selection, vol. 10, September 1997, pages 991-997

7: Strop et al: Engineering enzyme subsite specificity: preparation, kinetic characterization, and x-ray analysis at 2.0 ANG resolution of Val111phe site mutated calf chymosin, Biochemistry, vol. 29, October 1990, pages 9863-9871

8: Supannee et al: Site-specific mutations of calf chymosin B which influence milk-clotting activity, Food Chemistry, vol. 62, June 1998, pages 133-139

9: Zhang et al: Functional implications of disulfide bond, Cys45-Cys50, in recombinant prochymosin, Biochimica et biophysica acta, vol. 1343, December 1997, pages 278-286. 

1-15 (canceled)
 16. A method for making an isolated chymosin polypeptide variant comprising: (a) producing a chymosin polypeptide variant having an alteration at one or more positions in its amino acid sequence relative to a parent polypeptide having chymosin activity, wherein the parent polypeptide has at least 65% sequence identity with the mature polypeptide from amino acid position 59 to amino acid position 381 of SEQ ID NO: 1 (bovine chymosin), wherein the alteration comprises a substitution at an amino acid position corresponding to position 311 as determined by an alignment of the amino acid sequence of the parent polypeptide with the amino acid sequence of the polypeptide of SEQ ID NO: 1, and (b) isolating the polypeptide variant of step (a), thereby obtaining the isolated chymosin polypeptide variant, wherein the variant has fewer than 30 amino acid alterations in the region from amino acid position 59 to amino acid position 381 as compared to the mature polypeptide from amino acid position 59 to amino acid position 381 of SEQ ID NO: 1 or as compared to the mature polypeptide from amino acid position 59 to amino acid position 381of SEQ ID NO: 2 (camel chymosin), as determined by an alignment of the amino acid sequence of the variant with the amino acid sequence of SEQ ID NO: 1 or SEQ ID NO:2, respectively, and has chymosin activity.
 17. The method of claim 16, wherein the isolated chymosin polypeptide variant has a chymosin activity giving a higher clotting activity to proteolytical activity (C/P) ratio as compared to the C/P ratio of bovine chymosin comprising the mature polypeptide of SEQ ID NO: 1, and a chymosin activity giving a higher C/P ratio as compared to the C/P ratio of camel chymosin comprising the mature polypeptide of SEQ ID NO:
 2. 18. The method of claim 16, wherein the alteration comprises the amino acid substitution L311I.
 19. The method of claim 16, wherein the alteration comprises amino acid substitutions selected from: V261A+V263I+G309W+L311I+Y326F; Y79S+L224V+L311I; and R119S+V241I+L280I+L311I+D325M.
 20. The method of claim 16, wherein the parent polypeptide has at least 95% sequence identity with the mature polypeptide of SEQ ID NO:
 1. 21. The method of claim 16, wherein the parent polypeptide has at least 95% sequence identity with the mature polypeptide from amino acid position 59 to amino acid position 381 of SEQ ID NO:
 2. 22. An isolated chymosin polypeptide variant obtained by a method that comprises: (a) producing a chymosin polypeptide variant having an alteration at one or more positions in its amino acid sequence relative to a parent polypeptide having chymosin activity, wherein the parent polypeptide has at least 65% sequence identity with the mature polypeptide from amino acid position 59 to amino acid position 381of SEQ ID NO: 1 (bovine chymosin), wherein the alteration comprises a substitution at an amino acid position corresponding to position 311 as determined by an alignment of the amino acid sequence of the parent polypeptide with the amino acid sequence of the polypeptide of SEQ ID NO: 1; and (b) isolating the polypeptide variant of step (a), thereby obtaining the isolated chymosin polypeptide variant, wherein the variant has fewer than 30 amino acid alterations in the region from amino acid position 59 to amino acid position 381 as compared to the mature polypeptide from amino acid position 59 to amino acid position 381of SEQ ID NO: 1 or as compared to the mature polypeptide from amino acid position 59 to amino acid position 381of SEQ ID NO: 2, as determined by an alignment of the amino acid sequence of the variant with the amino acid sequence of SEQ ID NO: 1 or SEQ ID NO:2, respectively, and has chymosin activity.
 23. An isolated chymosin polypeptide variant having an alteration at one or more positions in its amino acid sequence relative to a parent polypeptide having chymosin activity, wherein the parent polypeptide has at least 90% sequence identity with the mature polypeptide from amino acid position 59 to amino acid position 381 of SEQ ID NO: 1 (bovine chymosin), wherein the alteration comprises a substitution at an amino acid position corresponding to position 311 as determined by an alignment of the amino acid sequence of the parent polypeptide with the amino acid sequence of the polypeptide of SEQ ID NO: 1, wherein: the variant has chymosin activity; the variant has less than 100% sequence identity with the mature polypeptide from amino acid position 59 to amino acid position 381 of SEQ ID NO: 1; and the variant has fewer than 30 amino acid alterations in the region from amino acid position 59 to amino acid position 381 as compared to the mature polypeptide from amino acid position 59 to amino acid position 381of SEQ ID NO: 1, as determined by an alignment of the amino acid sequence of the variant with the amino acid sequence of SEQ ID NO:
 1. 24. The isolated chymosin polypeptide variant of claim 23, wherein the parent polypeptide has at least 97% sequence identity with the mature polypeptide from amino acid position 59 to amino acid position 381 of SEQ ID NO: 1; and the isolated chymosin polypeptide variant comprises fewer than 10 amino acid alterations in the region from amino acid position 59 to amino acid position 381 as compared to the mature polypeptide from amino acid position 59 to amino acid position 381 of SEQ ID NO: 1, as determined by an alignment of the amino acid sequence of the variant with the amino acid sequence of SEQ ID NO:
 1. 25. The isolated chymosin polypeptide variant of claim 23, wherein the alteration comprises the amino acid substitution L311I.
 26. The isolated chymosin polypeptide variant of claim 23, wherein the alteration comprises amino acid substitutions selected from: V261A+V263I+G309W+L311I+Y326F; Y79S+L224V+L311I; and R119S+V241I+L280I+L311I+D325M.
 27. The isolated chymosin polypeptide variant of claim 23, wherein variant has a chymosin activity giving a higher clotting activity to proteolytical activity (C/P) ratio as compared to the C/P ratio of bovine chymosin comprising the mature polypeptide from amino acid position 59 to amino acid position 381 of SEQ ID NO:
 1. 28. An isolated chymosin polypeptide variant having an alteration at one or more positions in its amino acid sequence relative to a parent polypeptide having chymosin activity, wherein the parent polypeptide has at least 90% sequence identity with the mature polypeptide from amino acid position 59 to amino acid position 381 of SEQ ID NO: 2 (camel chymosin),wherein the alteration comprises a substitution at an amino acid position corresponding to position 311as determined by an alignment of the amino acid sequence of the parent polypeptide with the amino acid sequence of the polypeptide of SEQ ID NO: 1, wherein: the variant has chymosin activity; and the variant has less than 100% sequence identity with the mature polypeptide from amino acid position 59 to amino acid position 381 of SEQ ID NO: 2; and the variant has fewer than 30 amino acid alterations in the region from amino acid position 59 to amino acid position 381 as compared to the mature polypeptide from amino acid position 59 to amino acid position 381 of SEQ ID NO: 2, as determined by an alignment of the amino acid sequence of the variant with the amino acid sequence of SEQ ID NO:
 2. 29. The isolated chymosin polypeptide variant of claim 28, wherein the alteration comprises the amino acid substitution L311I.
 30. The isolated chymosin polypeptide variant of claim 28, wherein the alteration comprises amino acid substitutions selected from: V261A+V263I+G309W+L311I+Y326F; Y79S+L224V+L311I; and R119S+V241I+L280I+L311I+D325M.
 31. The isolated chymosin polypeptide variant of claim 28, wherein the variant has a chymosin activity giving a higher clotting activity to proteolytical activity (C/P) ratio as compared to the C/P ratio of Camel chymosin comprising the mature polypeptide from amino acid position 59 to amino acid position 381 of SEQ ID NO:
 2. 32. A method for making a milk-based food or feed product comprising adding an effective amount of the isolated chymosin polypeptide variant according to claim 23 to food or feed ingredient(s) comprising milk.
 33. The method for making a milk-based food or feed product according to claim 30, wherein the milk is selected from soya milk, sheep milk, goat milk, buffalo milk, yak milk, lama milk, camel milk and cow milk.
 34. The method for making a milk-based food or feed product according to claim 30, wherein the milk-based product is a fermented milk product, a quark or a cheese.
 35. A method for making a milk-based food or feed product comprising adding an effective amount of the isolated chymosin polypeptide variant according to claim 28 to food or feed ingredient(s) comprising milk.
 36. The method for making a milk-based food or feed product according to claim 35, wherein the milk is selected from soya milk, sheep milk, goat milk, buffalo milk, yak milk, lama milk, camel milk and cow milk.
 37. The method for making a milk-based food or feed product according to claim 35, wherein the milk-based product is a fermented milk product, a quark or a cheese. 